[Mristudio-users] ROI transformation

[Julie McEntee]

Try these steps in DiffeoMap:

Go to ŒAtlas Sample Images¹ on top toolbar
  Place curser over ŒJHU_MNI_SS¹, click ŒJHU_MNI_SS_WMPM_TypeII¹
Click ŒFile¹ on top toolbar; click ŒLoad SubjectŠ¹
  Navigate to ROIEditor/Images/JHU_MNI_SS; double-click
ŒJHU_MNI_SS_WMPM_TypeII.dat¹; click OK
In ŒJHU_MNI_SS_WMPM_TypeII.dat ­ Subject¹ window, under Transformation,
Automatic Image Registration
1)     Click Invert button
2)     Click AIR File button; navigate to subject¹s folder; double-click
ŒAlignlinearOutput_<subjectID>.air¹; click OK
Under ŒVolume LDDMM¹, ŒRemote (Send Data to the Server)¹, under ŒSingle
Channel¹ button; click 1st button on left with blue M and open folder icon
(Load Transformation Matrix)
1)     Choose LDDMM Matrix (VTK Format)
2)     Interpolation: Trilinear
3)     Click Browse button and navigate to subject¹s folder; click OK
4)     Navigate to subject¹s ŒResults¹ folder, choose Hmap.vtk; click Open;
click OK to change dimensions
5)     Result file (visable in drop-down menu under Image):
Lddmm_JHU_MNI_SS_WMPM_TypeII.dat
Click ŒLoad Transformation Matrix¹ button (blue ŒM¹ button)
1)     Choose AIR Linear Matrix
2)     Interpolation: Nearest Neighbor
3)     Click Browse button and navigate to subject¹s folder; click OK
4)     Choose Invert_AlignlinearOutput_<subjectID>.air; click Open
5)     Result file (visable in drop-down menu under Image):
Air_Lddmm_JHU_MNI_SS_WMPM_TypeII.dat

-Julie

Julie E. McEntee, MA, CCRP
Senior Research Program Coordinator
Department of Psychiatry- Neuroimaging
Johns Hopkins University School of Medicine
600 N. Wolfe St./Phipps 300
Baltimore, MD 21287
Phone: 410-502-0468
Fax: 410-614-3676



On 7/19/10 4:20 PM, "Josselin" <j.houenou at yahoo.fr> wrote:

> Dear mristudio developers and users,
> 
> I have a pretty trivial question but I couldn't find any way to do it.
> 
> I got for one subject a FA image and a B0 image. My goal is to register the
> WMPM type II eve atlas onto my FA map such as done in
> http://www.ncbi.nlm.nih.gov/pubmed/20570617 (paper by Zhang).
> 
> I therefore used the steps described in
> https://www.mristudio.org/wiki/user_manual/diffeomap/
> I coregistered my FA map and B0 map with air then LDDMM and obtained AIR and
> LDDDM matrices which seem correct: when I apply Hmap to the file named
> "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits
> perfectly well on my original FA map.
> 
> Nevertheless, I do not know how to transform the file
> "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is there any
> way to do it ? When I load this file as a "subject" in diffeomap and then try
> to apply Hmap.vtk onto it I get "Cannot crop the LDDMM map" as an error
> message. Any suggestion ??
> 
> Many thanks,
> Josselin Houenou
> 
> 
>       
> 
> 
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org